From: Heng Li <lh3@live.co.uk>
Date: Fri, 5 Nov 2010 15:28:23 +0000 (+0000)
Subject: Revert to r790. The recent changes are not good...
X-Git-Url: https://git.donarmstrong.com/?p=samtools.git;a=commitdiff_plain;h=2d2be1edb0548e95b771bc9c79cff48eb5d2e1f5

Revert to r790. The recent changes are not good...
---

diff --git a/bam2bcf.c b/bam2bcf.c
index ab5bfcd..509761d 100644
--- a/bam2bcf.c
+++ b/bam2bcf.c
@@ -3,6 +3,7 @@
 #include "bam.h"
 #include "kstring.h"
 #include "bam2bcf.h"
+#include "errmod.h"
 #include "bcftools/bcf.h"
 
 extern	void ks_introsort_uint32_t(size_t n, uint32_t a[]);
@@ -13,15 +14,18 @@ extern	void ks_introsort_uint32_t(size_t n, uint32_t a[]);
 
 #define CAP_DIST 25
 
+struct __bcf_callaux_t {
+	int max_bases, capQ, min_baseQ;
+	uint16_t *bases;
+	errmod_t *e;
+};
+
 bcf_callaux_t *bcf_call_init(double theta, int min_baseQ)
 {
 	bcf_callaux_t *bca;
 	if (theta <= 0.) theta = CALL_DEFTHETA;
 	bca = calloc(1, sizeof(bcf_callaux_t));
 	bca->capQ = 60;
-	bca->openQ = 40;
-	bca->extQ = 20;
-	bca->tandemQ = 100;
 	bca->min_baseQ = min_baseQ;
 	bca->e = errmod_init(1. - theta);
 	return bca;
@@ -53,7 +57,7 @@ int bcf_call_glfgen(int _n, const bam_pileup1_t *pl, int ref_base /*4-bit*/, bcf
 		const bam_pileup1_t *p = pl + i;
 		int q, b, mapQ, baseQ, is_diff, min_dist;
 		// set base
-		if (p->is_del || p->is_refskip || (p->b->core.flag&BAM_FUNMAP)) continue;
+		if (p->is_del || (p->b->core.flag&BAM_FUNMAP)) continue; // skip unmapped reads and deleted bases
 		baseQ = q = (int)bam1_qual(p->b)[p->qpos]; // base quality
 		if (q < bca->min_baseQ) continue;
 		mapQ = p->b->core.qual < bca->capQ? p->b->core.qual : bca->capQ;
@@ -83,125 +87,11 @@ int bcf_call_glfgen(int _n, const bam_pileup1_t *pl, int ref_base /*4-bit*/, bcf
 	return r->depth;
 }
 
-int bcf_call_glfgen_gap(int pos, int _n, const bam_pileup1_t *pl, bcf_callaux_t *bca, bcf_callret1_t *r)
-{
-	int i, n, n_ins, n_del;
-	memset(r, 0, sizeof(bcf_callret1_t));
-	if (_n == 0) return -1;
-
-	// enlarge the bases array if necessary
-	if (bca->max_bases < _n) {
-		bca->max_bases = _n;
-		kroundup32(bca->max_bases);
-		bca->bases = (uint16_t*)realloc(bca->bases, 2 * bca->max_bases);
-	}
-	// fill the bases array
-	memset(r, 0, sizeof(bcf_callret1_t));
-	r->indelreg = 10000;
-	n_ins = n_del = 0;
-	for (i = n = 0; i < _n; ++i) {
-		const bam_pileup1_t *p = pl + i;
-		int q, b, mapQ, indelQ, is_diff, min_dist;
-		if (p->is_del || p->is_refskip || (p->b->core.flag&BAM_FUNMAP)) continue;
-		{ // compute indel (base) quality
-			// this can be made more efficient, but realignment is the bottleneck anyway
-			int j, k, x, y, op, len = 0, max_left, max_rght, seqQ, indelreg;
-			bam1_core_t *c = &p->b->core;
-			uint32_t *cigar = bam1_cigar(p->b);
-			uint8_t *qual = bam1_qual(p->b);
-			for (k = y = 0, x = c->pos; k < c->n_cigar && y <= p->qpos; ++k) {
-				op = cigar[k]&0xf;
-				len = cigar[k]>>4;
-				if (op == BAM_CMATCH) {
-					if (pos > x && pos < x + len) break;
-					x += len; y += len;
-				} else if (op == BAM_CINS || op == BAM_CSOFT_CLIP) y += len;
-				else if (op == BAM_CDEL || op == BAM_CREF_SKIP) x += len;
-			}
-			if (k == c->n_cigar) continue; // this actually should not happen
-			max_left = max_rght = 0; indelreg = 0;
-			if (pos == x + len - 1 && k+2 < c->n_cigar && ((cigar[k+1]&0xf) == BAM_CINS || (cigar[k+1]&0xf) == BAM_CDEL)
-				&& (cigar[k+2]&0xf) == BAM_CMATCH)
-			{
-				for (j = y; j < y + len; ++j)
-					if (max_left < qual[j]) max_left = qual[j];
-				if ((cigar[k+1]&0xf) == BAM_CINS) y += cigar[k+1]>>4;
-				else x += cigar[k+1]>>4;
-				op = cigar[k+2]&0xf; len = cigar[k+2]>>4;
-				for (j = y; j < y + len; ++j) {
-					if (max_rght < qual[j]) max_rght = qual[j];
-					if (qual[j] > BAM2BCF_INDELREG_THRES && indelreg == 0)
-						indelreg = j - y + 1;
-				}
-				if (r->indelreg > indelreg) r->indelreg = indelreg;
-			} else {
-				for (j = y; j <= p->qpos; ++j)
-					if (max_left < qual[j]) max_left = qual[j];
-				for (j = p->qpos + 1; j < y + len; ++j)
-					if (max_rght < qual[j]) max_rght = qual[j];
-					
-			}
-			indelQ = max_left < max_rght? max_left : max_rght;
-			// estimate the sequencing error rate
-			seqQ = bca->openQ;
-			if (p->indel != 0) seqQ += bca->extQ * (abs(p->indel) - 1); // FIXME: better to model homopolymer
-			if (p->indel > 0) {
-				++n_ins; r->ins_len += p->indel;
-			} else if (p->indel < 0) {
-				++n_del; r->del_len += -p->indel;
-			}
-			if (p->indel != 0) { // a different model for tandem repeats
-				uint8_t *seq = bam1_seq(p->b);
-				int tandemQ, qb = bam1_seqi(seq, p->qpos), l;
-				for (j = p->qpos + 1; j < c->l_qseq; ++j)
-					if (qb != bam1_seqi(seq, j)) break;
-				l = j;
-				for (j = (int)p->qpos - 1; j >= 0; --j)
-					if (qb != bam1_seqi(seq, j)) break;
-				l = l - (j + 1);
-				tandemQ = (int)((double)(abs(p->indel)) / l * bca->tandemQ + .499);
-				if (seqQ > tandemQ) seqQ = tandemQ;
-			}
-//			fprintf(stderr, "%s\t%d\t%d\t%d\t%d\t%d\t%d\n", bam1_qname(p->b), pos+1, p->indel, indelQ, seqQ, max_left, max_rght);
-			if (indelQ > seqQ) indelQ = seqQ;
-			q = indelQ;
-		}
-		if (q < bca->min_baseQ) continue;
-		mapQ = p->b->core.qual < bca->capQ? p->b->core.qual : bca->capQ;
-		if (q > mapQ) q = mapQ;
-		if (q > 63) q = 63;
-		if (q < 4) q = 4;
-		b = p->indel? 1 : 0;
-		bca->bases[n++] = q<<5 | (int)bam1_strand(p->b)<<4 | b;
-		// collect annotations
-		r->qsum[b] += q;
-		is_diff = b;
-		++r->anno[0<<2|is_diff<<1|bam1_strand(p->b)];
-		min_dist = p->b->core.l_qseq - 1 - p->qpos;
-		if (min_dist > p->qpos) min_dist = p->qpos;
-		if (min_dist > CAP_DIST) min_dist = CAP_DIST;
-		r->anno[1<<2|is_diff<<1|0] += indelQ;
-		r->anno[1<<2|is_diff<<1|1] += indelQ * indelQ;
-		r->anno[2<<2|is_diff<<1|0] += mapQ;
-		r->anno[2<<2|is_diff<<1|1] += mapQ * mapQ;
-		r->anno[3<<2|is_diff<<1|0] += min_dist;
-		r->anno[3<<2|is_diff<<1|1] += min_dist * min_dist;
-	}
-	r->depth = n;
-	r->ins_len = n_ins? r->ins_len / n_ins : 0;
-	r->del_len = n_del? r->del_len / n_del : 0;
-	if (r->indelreg >= 10000) r->indelreg = 0;
-	// glfgen
-	errmod_cal(bca->e, n, 2, bca->bases, r->p);
-	return r->depth;	
-}
-
 int bcf_call_combine(int n, const bcf_callret1_t *calls, int ref_base /*4-bit*/, bcf_call_t *call)
 {
 	int ref4, i, j, qsum[4];
 	int64_t tmp;
 	call->ori_ref = ref4 = bam_nt16_nt4_table[ref_base];
-	call->ins_len = call->del_len = 0; call->indelreg = 0;
 	if (ref4 > 4) ref4 = 4;
 	// calculate qsum
 	memset(qsum, 0, 4 * sizeof(int));
@@ -264,66 +154,6 @@ int bcf_call_combine(int n, const bcf_callret1_t *calls, int ref_base /*4-bit*/,
 	return 0;
 }
 
-int bcf_call_combine_gap(int n, const bcf_callret1_t *calls, bcf_call_t *call)
-{
-	int i, j, n_ins, n_del;
-	// combine annotations
-	call->ori_ref = 4;
-	memset(call->anno, 0, 16 * sizeof(int));
-	call->ins_len = call->del_len = 0; call->indelreg = 10000;
-	for (i = call->depth = 0, n_ins = n_del = 0; i < n; ++i) {
-		const bcf_callret1_t *r = calls + i;
-		if (r->depth > 0) {
-			call->depth += r->depth;
-			if (r->ins_len > 0) {
-				call->ins_len += r->ins_len;
-				++n_ins;
-			}
-			if (r->del_len > 0) {
-				call->del_len += r->del_len;
-				++n_del;
-			}
-			if (r->indelreg > 0 && call->indelreg > r->indelreg)
-				call->indelreg = r->indelreg;
-			for (j = 0; j < 16; ++j) call->anno[j] += r->anno[j];
-		}
-	}
-	if (call->depth == 0) return 0; // no indels
-	call->ins_len = n_ins? call->ins_len / n_ins : 0;
-	call->del_len = n_del? call->del_len / n_del : 0;
-	//
-	for (i = 0; i < 5; ++i) call->a[i] = -1;
-	call->a[0] = 0; call->a[1] = 1;
-	call->unseen = -1;
-	call->n_alleles = 2;
-	// set the PL array
-	if (call->n < n) {
-		call->n = n;
-		call->PL = realloc(call->PL, 15 * n);
-	}
-	{
-		int g[3];
-		double sum_min = 0.;
-		g[0] = 0; g[1] = 1; g[2] = 3;
-		for (i = 0; i < n; ++i) {
-			uint8_t *PL = call->PL + 3 * i;
-			const bcf_callret1_t *r = calls + i;
-			float min = 1e37;
-			for (j = 0; j < 3; ++j)
-				if (min > r->p[g[j]]) min = r->p[g[j]];
-			sum_min += min;
-			for (j = 0; j < 3; ++j) {
-				int y;
-				y = (int)(r->p[g[j]] - min + .499);
-				if (y > 255) y = 255;
-				PL[j] = y;
-			}
-		}
-		call->shift = (int)(sum_min + .499);
-	}
-	return 0;
-}
-
 int bcf_call2bcf(int tid, int pos, bcf_call_t *bc, bcf1_t *b, bcf_callret1_t *bcr, int is_SP)
 {
 	extern double kt_fisher_exact(int n11, int n12, int n21, int n22, double *_left, double *_right, double *two);
@@ -333,19 +163,11 @@ int bcf_call2bcf(int tid, int pos, bcf_call_t *bc, bcf1_t *b, bcf_callret1_t *bc
 	b->tid = tid; b->pos = pos; b->qual = 0;
 	s.s = b->str; s.m = b->m_str; s.l = 0;
 	kputc('\0', &s);
-	if (bc->ins_len > 0 || bc->del_len > 0) { // an indel
-		for (i = 0; i < bc->indelreg; ++i) kputc('N', &s);
-		kputc('\0', &s);
-		if (bc->ins_len > 0 && bc->del_len > 0) kputs("<INDEL>", &s);
-		else if (bc->ins_len > 0) kputs("<INS>", &s);
-		else if (bc->del_len > 0) kputs("<DEL>", &s);
-	} else { // SNP
-		kputc("ACGTN"[bc->ori_ref], &s); kputc('\0', &s);
-		for (i = 1; i < 5; ++i) {
-			if (bc->a[i] < 0) break;
-			if (i > 1) kputc(',', &s);
-			kputc(bc->unseen == i? 'X' : "ACGT"[bc->a[i]], &s);
-		}
+	kputc("ACGTN"[bc->ori_ref], &s); kputc('\0', &s);
+	for (i = 1; i < 5; ++i) {
+		if (bc->a[i] < 0) break;
+		if (i > 1) kputc(',', &s);
+		kputc(bc->unseen == i? 'X' : "ACGT"[bc->a[i]], &s);
 	}
 	kputc('\0', &s);
 	kputc('\0', &s);
diff --git a/bam2bcf.h b/bam2bcf.h
index b6514c0..4de743a 100644
--- a/bam2bcf.h
+++ b/bam2bcf.h
@@ -2,23 +2,13 @@
 #define BAM2BCF_H
 
 #include <stdint.h>
-#include "errmod.h"
 #include "bcftools/bcf.h"
 
-#define BAM2BCF_INDELREG_THRES 13
-
-typedef struct __bcf_callaux_t {
-	int max_bases, capQ, min_baseQ;
-	int openQ, extQ, tandemQ;
-	// for internal uses
-	uint16_t *bases;
-	errmod_t *e;
-} bcf_callaux_t;
+struct __bcf_callaux_t;
+typedef struct __bcf_callaux_t bcf_callaux_t;
 
 typedef struct {
-	int depth, indelreg;
-	float ins_len, del_len;
-	int qsum[4];
+	int depth, qsum[4];
 	int anno[16];
 	float p[25];
 } bcf_callret1_t;
@@ -26,9 +16,7 @@ typedef struct {
 typedef struct {
 	int a[5]; // alleles: ref, alt, alt2, alt3
 	int n, n_alleles, shift, ori_ref, unseen;
-	int indelreg;
-	float ins_len, del_len;
-	int depth, anno[16];
+	int anno[16], depth;
 	uint8_t *PL;
 } bcf_call_t;
 
@@ -40,9 +28,7 @@ extern "C" {
 	void bcf_call_destroy(bcf_callaux_t *bca);
 	int bcf_call_glfgen(int _n, const bam_pileup1_t *pl, int ref_base /*4-bit*/, bcf_callaux_t *bca, bcf_callret1_t *r);
 	int bcf_call_combine(int n, const bcf_callret1_t *calls, int ref_base /*4-bit*/, bcf_call_t *call);
-	int bcf_call_combine_gap(int n, const bcf_callret1_t *calls, bcf_call_t *call);
 	int bcf_call2bcf(int tid, int pos, bcf_call_t *bc, bcf1_t *b, bcf_callret1_t *bcr, int is_SP);
-	int bcf_call_glfgen_gap(int pos, int _n, const bam_pileup1_t *pl, bcf_callaux_t *bca, bcf_callret1_t *r);
 
 #ifdef __cplusplus
 }
diff --git a/bam_plcmd.c b/bam_plcmd.c
index 32d050d..a3e6aeb 100644
--- a/bam_plcmd.c
+++ b/bam_plcmd.c
@@ -729,29 +729,6 @@ static int mpileup(mplp_conf_t *conf, int n, char **fn)
 			bcf_call2bcf(tid, pos, &bc, b, (conf->flag&(MPLP_FMT_DP|MPLP_FMT_SP))? bcr : 0, (conf->flag&MPLP_FMT_SP));
 			bcf_write(bp, bh, b);
 			bcf_destroy(b);
-			// test if there is an indel
-			if (conf->flag&MPLP_REALN) {
-				for (i = 0; i < gplp.n; ++i) {
-					int j;
-					for (j = 0; j < gplp.n_plp[i]; ++j) {
-						const bam_pileup1_t *p = gplp.plp[i] + j;
-						if (p->indel != 0) break;
-					}
-					if (j != gplp.n_plp[i]) break;
-				}
-				if (i < gplp.n) { // at least one of the read contains a gap
-					for (i = 0; i < gplp.n; ++i)
-						bcf_call_glfgen_gap(pos, gplp.n_plp[i], gplp.plp[i], bca, bcr + i);
-					bcf_call_combine_gap(gplp.n, bcr, &bc);
-					if (bc.depth > 0) {
-						b = calloc(1, sizeof(bcf1_t));
-						bcf_call2bcf(tid, pos, &bc, b, (conf->flag&(MPLP_FMT_DP|MPLP_FMT_SP))? bcr : 0,
-									 (conf->flag&MPLP_FMT_SP));
-						bcf_write(bp, bh, b);
-						bcf_destroy(b);
-					}
-				}
-			}
 		} else {
 			printf("%s\t%d\t%c", h->target_name[tid], pos + 1, (ref && pos < ref_len)? ref[pos] : 'N');
 			for (i = 0; i < n; ++i) {